Alignments for a candidate for fadA in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Dyella japonica UNC79MFTsu3.2

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate N515DRAFT_2688 N515DRAFT_2688 acetyl-CoA acyltransferase

Query= SwissProt::O32177
         (391 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2688
          Length = 401

 Score =  370 bits (950), Expect = e-107
 Identities = 199/401 (49%), Positives = 264/401 (65%), Gaps = 18/401 (4%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59
           +++A IV+  RTPVGKA +G     RPDD+ A  ++  + +A G + + I D+I+GCA P
Sbjct: 5   VQDAYIVAATRTPVGKAPRGVFRNTRPDDMLAHVIRAVMAQAPGIDAHRIGDVIVGCAMP 64

Query: 60  EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119
           EAEQG+N+AR    LAGLP TVP +TVNR+CSSG+Q+IA AA++I LG  D  IA G ES
Sbjct: 65  EAEQGMNVARIGLLLAGLPDTVPGVTVNRFCSSGVQAIAQAADRIRLGEADLMIAAGTES 124

Query: 120 MSQVPMMGHVTRPNLALAEKAP-EYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAK 178
           MS VPMMGH    N  + +         MG TAE VAK++ +SRE+QD FA  SH+ A  
Sbjct: 125 MSMVPMMGHKVAMNPGIFDNEHIGIAYGMGITAENVAKQWKISREEQDTFAAASHERALA 184

Query: 179 ALAEGKFKDEIVPVEVTVTEIGEDHKP-------MEKQFVFSQDEGVRPQTTADILSTLR 231
           A+  G+FKDEI P ++      +DH P            +   DEG RP +T ++L  L+
Sbjct: 185 AIKAGEFKDEITPFKL------DDHYPDLATRSIKTDSRLIDTDEGPRPGSTVEVLGKLK 238

Query: 232 PAF---SVDGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMG 288
           P F      G+VTAGNSSQTSDGA AV+L         GL P+ +F S++V GV P++MG
Sbjct: 239 PVFRNGQFGGSVTAGNSSQTSDGAGAVLLASEAAIKEYGLTPIARFVSYSVAGVRPDIMG 298

Query: 289 IGPVEAIPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHP 348
           IGP EAIP+ALK AG+    +   ELNEAFA+Q++ VI++LG+D  K+N  GGAIALGHP
Sbjct: 299 IGPKEAIPKALKQAGMTQDQLDWIELNEAFAAQSLAVIKDLGLDPSKINPLGGAIALGHP 358

Query: 349 LGCTGTKLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
           LG TG     +L+H M+RR +++G+VTMCIG GMGAAG+FE
Sbjct: 359 LGATGAIRAATLVHGMRRRKQKYGMVTMCIGTGMGAAGIFE 399


Lambda     K      H
   0.316    0.133    0.377 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 421
Number of extensions: 14
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 391
Length of database: 401
Length adjustment: 31
Effective length of query: 360
Effective length of database: 370
Effective search space:   133200
Effective search space used:   133200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate N515DRAFT_2688 N515DRAFT_2688 (acetyl-CoA acyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01930.hmm
# target sequence database:        /tmp/gapView.13990.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                    Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.3e-146  473.6   1.5   2.6e-146  473.4   1.5    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2688  N515DRAFT_2688 acetyl-CoA acyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2688  N515DRAFT_2688 acetyl-CoA acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  473.4   1.5  2.6e-146  2.6e-146       1     385 []      10     399 ..      10     399 .. 0.97

  Alignments for each domain:
  == domain 1  score: 473.4 bits;  conditional E-value: 2.6e-146
                                    TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaRe 63 
                                                  iv+a+Rtp+g + +g++++++++d+la+vi++++++a g+d+++i +vi+G++++++eq +n+aR 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2688  10 IVAATRTPVGkAPRGVFRNTRPDDMLAHVIRAVMAQApGIDAHRIGDVIVGCAMPEAEQgMNVARI 75 
                                                  8*********988***************************************************** PP

                                    TIGR01930  64 aalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrresl 129
                                                   +l aglp++vp++tvnr+C+Sg+qA+a+aa++i+ Gead+++a+G EsmS vp++ ++      +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2688  76 GLLLAGLPDTVPGVTVNRFCSSGVQAIAQAADRIRLGEADLMIAAGTESMSMVPMMGHK----VAM 137
                                                  ******************************************************96665....699 PP

                                    TIGR01930 130 klgkakledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivp 195
                                                  ++g +++e+         ++ mg+tAen+ak+++isReeqD +a++Sh++a +Ai++g+fkdei+p
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2688 138 NPGIFDNEH------IGIAYGMGITAENVAKQWKISREEQDTFAAASHERALAAIKAGEFKDEITP 197
                                                  ******999......6678*********************************************** PP

                                    TIGR01930 196 vevkgk............kkvvskDegirpnttlekLakLkpafke..kkgstvtAgNssqlnDGA 247
                                                  +++ ++            ++ +++Deg+rp++t+e L+kLkp+f++    g  vtAgNssq++DGA
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2688 198 FKLDDHypdlatrsiktdSRLIDTDEGPRPGSTVEVLGKLKPVFRNgqFGG-SVTAGNSSQTSDGA 262
                                                  ***999**********99999***********************9853335.6************* PP

                                    TIGR01930 248 aalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAF 313
                                                  +a+ll+se++ ke+gltp+ar+vs++vagv p++mg+gp +Ai+kaLk+ag++ +++d++E+nEAF
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2688 263 GAVLLASEAAIKEYGLTPIARFVSYSVAGVRPDIMGIGPKEAIPKALKQAGMTQDQLDWIELNEAF 328
                                                  ****************************************************************** PP

                                    TIGR01930 314 AaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqG 379
                                                  Aaq lav+k+lg ld++k+N  GGAiAlGHPlGa+Ga+  +tl++ +++r++kyG++t+C+g+G+G
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2688 329 AAQSLAVIKDLG-LDPSKINPLGGAIALGHPLGATGAIRAATLVHGMRRRKQKYGMVTMCIGTGMG 393
                                                  ************.99*************************************************** PP

                                    TIGR01930 380 aAvile 385
                                                  aA i+e
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2688 394 AAGIFE 399
                                                  ***997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (401 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.53
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources